Chemical Biology of Peptide Nucleic Acids (PNAs)

The Chemical Biology of Nucleic Acids

Volumn , Issue , 2010, Pages 103-113

  Nielsen, Peter E ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Gene targeting and PNAs gene therapeutic drug discovery; Homopyrimidine PNAs binding to complementary homopurine targets; Origin of life PNAs prebiotic synthesis; Peptide conjugation improving PNAs based drug in vivo activity; Peptide nucleic acids (PNAs), DNA analogues chemical biology; PNA oligomers cellular and in vivo delivery; PNAs applications hybridization probes and genetic diagnostic tools; RNA interference sequence directed and dependent interference with RNA function; RNA interference based antibacterial drugs development; Somatic gene repair inducers site specific double stranded genomic DNA breaks

Indexed keywords

EID: 84886221635     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470664001.ch5     Document Type: Chapter

References (76)

1. Nielsen PE, Egholm M, Berg RH, Buchardt O, Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science 1991, 254, 1497-1500.
2. Egholm M, Buchardt O, Nielsen PE, Berg RH, Peptide nucleic acids (PNA). Oligonucleotide analogs with an achiral peptide backbone. Journal of the American Chemical Society 1992, 114, 1895-1897.
3. Ganesh KN, Nielsen PE, Peptide nucleic acids: analogs and derivatives. Current Organic Chemistry 2000, 4, 931-943.
4. Nielsen E, RNA targeting using peptide nucleic acid. In RNA Towards Medicine, ed. Erdmann V, Brosius J, Barciszewski J, Springer, Berlin, 2006, pp. 395-403.
5. Sazani P, Kang SH, Maier MA, Wei C, Dillman J, Summerton J, Manoharan M, Kole R, Nuclear antisense effects of neutral, anionic and cationic oligonucleotide analogs. Nucleic Acids Res 2001, 29, 3965-3974.
6. Karras JG, Maier MA, Lu T, Watt A, Manoharan M, Peptide nucleic acids are potent modulators of endogenous pre-mRNA splicing of the murine interleukin-5 receptor-alpha chain. Biochemistry 2001, 40, 7853-7859.
7. Sazani P, Astriab-Fischer A, Kole R, Effects of base modifications on antisense properties of 20-O-methoxyethyl and PNA oligonucleotides. Antisense and Nucleic Acid Drug Development 2003, 13, 119-128.
8. Siwkowski AM, Malik L, Esau CC, Maier MA, Wancewicz EV, Albertshofer K, Monia BP, Bennett CF, Eldrup AB, Identification and functional validation of PNAs that inhibit murine CD40 expression by redirection of splicing. Nucleic Acids Research 2004, 32, 2695-2706.
9. Wilusz JE, Devanney SC, Caputi M, Chimeric peptide nucleic acid compounds modulate splicing of the bcl-x gene in vitro and in vivo. Nucleic Acids Research 2005, 33, 6547-6554.
10. Shiraishi T, Pankratova S, Nielsen PE, Calcium ions effectively enhance the effect of antisense peptide nucleic acids conjugated to cationic tat and oligoarginine peptides. Chemistry and Biology 2005, 12, 923-929.
11. Fabani MM, Gait MJ, miR-122 targeting with LNA/20-O-methyl oligonucleotide mixmers, peptide nucleic acids (PNA) and PNA-peptide conjugates. RNA 2008, 14, 336-346.
12. Yin H, Lu Q, Wood M, Effective exon skipping and restoration of dystrophin expression by peptide nucleic acid antisense oligonucleotides in mdx mice. Molecular Therapy 2008, 16, 38-45.
13. Wolf Y, Pritz S, Abes S, Bienert M, Lebleu B, Oehlke J, Structural requirements for cellular uptake and antisense activity of peptide nucleic acids conjugated with various peptides. Biochemistry 2006, 45, 14944-14954.
14. Nielsen PE, Egholm M, Buchardt O, Evidence for (PNA)2/DNA triplex structure upon binding of PNA to dsDNA by strand displacement. Journal of Molecular Recognition 1994, 7, 165-170.
15. Demidov VV, Yavnilovich MV, Belotserkovskii BP, Frank-Kamenetskii MD, Nielsen PE, Kinetics and mechanism of polyamide ('peptide') nucleic acid binding to duplex DNA. Proceedings of the National Academy of Sciences of the United States of America 1995, 92, 2637-2641.
16. Nielsen PE, Christensen L, Strand displacement binding of a duplex-forming homopurine PNA to a homopyrimidine duplex DNA target. Journal of the American Chemical Society 1996, 118, 2287-2288.
17. Lohse J, Dahl O, Nielsen PE, Double duplex invasion by peptide nucleic acid: a general principle for sequencespecific targeting of double-stranded DNA. Proceedings of the National Academy of Sciences of the United States of America 1999, 96, 11804-11808.
18. Hansen ME, Bentin T, Nielsen PE, High-affinity triplex targeting of double stranded DNA Using chemically modified peptide nucleic acid oligomers. Nucleic Acids Research 2009, 37, 4498-4507.
19. Ishizuka T, Yoshida J, Yamamoto Y, Sumaoka J, Tedeschi T, Corradini R, Sforza S, Komiyama M, Chiral introduction of positive charges to PNA for double-duplex invasion to versatile sequences. Nucleic Acids Research 2008, 36, 1464-1471.
20. Rapireddy S, He G, Roy S, Armitage BA, Ly DH, Strand invasion of mixed-sequence B-DNA by acridinelinked, gamma-peptide nucleic acid (gamma-PNA). Journal of the American Chemical Society 2007, 129, 15596-15600.
21. Roy S, Tanious FA, Wilson WD, Ly DH, Armitage BA, High-affinity homologous peptide nucleic acid probes for targeting a quadruplex-forming sequence from a MYC promoter element. Biochemistry 2007, 46, 10433-10443.
22. Nielsen PE, Egholm M, Buchardt O, Sequence-specific transcription arrest by peptide nucleic acid bound to the DNA template strand. Gene 1994, 149, 139-145.
23. Hanvey JC, Peffer NJ, Bisi JE, Thomson SA, Cadilla R, Josey JA, Ricca DJ, Hassman CF, Bonham MA, Antisense and antigen properties of peptide nucleic acids. Science 1992, 258, 1481-1485.
24. Janowski BA, Kaihatsu K, Huffman KE, Schwartz JC, Ram R, Hardy D, Mendelson CR, Corey DR, Inhibiting transcription of chromosomal DNA with antigene peptide nucleic acids. Nature Chemical Biology 2005, 1, 210-215.
25. Milne L, Xu Y, Perrin DM, Sigman DS, An approach to gene-specific transcription inhibition using oligonucleotides complementary to the template strand of the open complex. Proceedings of the National Academy of Sciences of the United States of America 2000, 97, 3136-3141.
26. Urnov FD, Miller JC, Lee YL, Beausejour CM, Rock JM, Augustus S, Jamieson AC, Porteus MH, Gregory PD, Holmes MC. Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 2005, 435, 646-651.
27. Lombardo A, Genovese P, Beausejour CM, Colleoni S, Lee YL, Kim KA, Ando D, Urnov FD, Galli C, Gregory PD, Holmes MC, Naldini L. Gene editing in human stem cells using zinc finger nucleases and integrase-defective lentiviral vector delivery. Nature Biotechnology 2007; 25, 1298-1306.
28. Chin JY, Kuan JY, Lonkar PS, Krause DS, Seidman MM, Peterson KR, Nielsen PE, Kole R, Glazer PM, Correction of a splice-site mutation in the beta-globin gene stimulated by triplex-forming peptide nucleic acids. Proceedings of the National Academy of Sciences of the United States of America 2008, 105, 13514-13519.
29. Good L, Nielsen PE, Antisense inhibition of gene expression in bacteria by PNA targeted to mRNA. Nature Biotechnology 1998, 16, 355-358.
30. Good L, Awasthi SK, Dryselius R, Larsson O, Nielsen PE, Bactericidal antisense effects of peptide-PNA conjugates. Nature Biotechnology 2001, 19, 360-364.
31. Dryselius R, Aswasti SK, Rajarao GK, Nielsen PE, Good L, The translation start codon region is sensitive to antisense PNA inhibition in Escherichia coli. Oligonucleotides 2003, 13, 427-433.
32. Dryselius R, Nekhotiaeva N, Nielsen PE, Good L, Antibiotic-free bacterial strain selection using antisense peptide nucleic acid. BioTechniques 2003, 35, 1060-1064.
33. Geller BL, Antibacterial antisense. Current Opinion in Molecular Therapeutics 2005, 7, 109-113.
34. Nikravesh A, Dryselius R, Faridani OR, Goh S, Sadeghizadeh M, Behmanesh M, Ganyu A, Klok EJ, Zain R, Good L, Antisense PNA accumulates in Escherichia coli and mediates a long post-antibiotic effect. Molecular Therapy 2007, 15, 1537-1542.
35. Kurupati P., Tan KS, Kumarasinghe G, Poh CL, Inhibition of gene expression and growth by antisense peptide nucleic acids in a multiresistant beta-lactamase-producing Klebsiella pneumoniae strain. Antimicrobial Agents and Chemotherapy 2007, 51, 805-811.
36. Nekhotiaeva N, Awasthi SK, Nielsen PE, Good L, Inhibition of Staphylococcus aureus gene expression and growth using antisense peptide nucleic acids. Molecular Therapy 2004, 10, 652-659.
37. Tan XX, Actor JK, Chen Y, Peptide nucleic acid antisense oligomer as a therapeutic strategy against bacterial infection: proof of principle using mouse intraperitoneal infection. Antimicrobial Agents and Chemotherapy 2005, 49, 3203-3207.
38. Good L, Nielsen PE, Inhibition of translation and bacterial growth by peptide nucleic acid targeted to ribosomal RNA. Proceedings of the National Academy of Sciences of the United States of America 1998, 95, 2073-2076.
39. Huang XW, Pan J, An XY, Zhuge HX, Inhibition of bacterial translation and growth by peptide nucleic acids targeted to domain II of 23S rRNA. Journal of Peptide Science 2007, 13, 220-226.
40. Hamzavi R, Dolle F, Tavitian B, Dahl O, Nielsen PE, Modulation of the pharmacokinetic properties of PNA: preparation of galactosyl, mannosyl, fucosyl, N-acetylgalactosaminyl and N-acetylglucosaminyl derivatives of aminoethylglycine peptide nucleic acid monomers and their incorporation into PNA oligomers. Bioconjugate Chemistry 2003, 14, 941-954.
41. Abes R, Arzumanov AA, Moulton HM, Abes S, Ivanova GD, Iversen PL, Gait MJ, Lebleu B, Cell-penetratingpeptide- based delivery of oligonucleotides: an overview. Biochemical Society Transactions 2007, 35, 775-779.
42. Abes S, Turner JJ, Ivanova GD, Owen D, Williams D, Arzumanov A, Clair P, Gait MJ, Lebleu B, Efficient splicing correction by PNA conjugation to an R6-penetratin delivery peptide. Nucleic Acids Research 2007, 35, 4495-4502.
43. Pooga M, Soomets U, Hällbrink M, Valkna A, Saar K, Rezaei K, Kahl U, Hao JX, Xu XJ, Wisenfeld-Hallin Z, Hökfelt T, Bartfai T, Langel Ü , Cell penetrating PNA constructs regulate galanin receptor levels and modify pain transmission in vivo. Nature Biotechnology 1998, 16, 857-861.
44. Bendifallah N, Rasmussen FW, Zachar V, Ebbesen P, Nielsen PE, Koppelhus U, Evaluation of cell-penetrating peptides (CPPs) as vehicles for intracellular delivery of antisense peptide nucleic acid (PNA). Bioconjugate Chemistry 2006, 17, 750-758.
45. El-Andaloussi S, Johansson HJ, Holm T, LangelÜ , A novel cell-penetrating peptide, M918, for efficient delivery of proteins and peptide nucleic acids. Molecular Therapy 2007, 15, 1820-1826.
46. Shiraishi T, Hamzavi R, Nielsen PE, Subnanomolar antisense activity of phosphonate-peptide nucleic acid (PNA) conjugates delivered by cationic lipids to HeLa cells. Nucleic Acids Research 2008, 36, 4424-4432.
47. Abes S, Williams D, Prevot P, Thierry A, Gait MJ, Lebleu B, Endosome trapping limits the efficiency of splicing correction by PNA-oligolysine conjugates. Journal of Controlled Release 2006, 110, 595-604.
48. Shiraishi T, Nielsen PE, Photochemically enhanced cellular delivery of cell penetrating peptide-PNA conjugates. FEBS Letters 2006, 580, 1451-1456.
49. Shiraishi T, Nielsen PE, Enhanced delivery of cell-pepetrating peptide-peptide nucleic acid conjugates by endosomal disruption. Nature Protocols 2006, 1, 633-636.
50. Ivanova GD, Arzumanov A, Abes R, Yin H, Wood MJ, Lebleu B, Gait MJ, Improved cell-penetrating peptide-PNA conjugates for splicing redirection in HeLa cells and exon skipping in mdx mouse muscle. Nucleic Acids Research 2008, 36, 6418-6428.
51. Koppelhus U, Shiraishi T, Zachar V, Pankratova S, Nielsen PE, Improved cellular activity of antisense peptide nucleic acids by conjugation to a cationic peptide-lipid (CatLip) domain. Bioconjugate Chemistry 2008, 19, 1526-1534.
52. Hu J, Corey DR, Inhibiting gene expression with peptide nucleic acid (PNA)-peptide conjugates that target chromosomal DNA. Biochemistry 2007, 46, 7581-7589.
53. Wright DG, Zhang Y, Murphy JR, Effective delivery of antisense peptide nucleic acid oligomers into cells by anthrax protective antigen. Biochemical and Biophysical Research Communications 2008, 376, 200-205.
54. Sazani P, Gemignani F, Kang S-H, Maier MA, Manoharan M, Persmark M, Bortner D, Kole R, Systemically delivered antisense oligomers upregulate gene expression in mouse tissues. Nature Biotechnology 2002, 20, 1228-1233.
55. Boffa LC, Cutrona G, Cilli M, Matis S, Damonte G,MMariani. R, Millo E, Moroni M, Roncella S, Fedeli F, Ferrarini M, Inhibition of Burkitt's lymphoma cells growth in SCID mice by a PNA specific for a regulatory sequence of the translocated c-myc. Cancer Gene Therapy 2007, 14, 220-226.
56. McMahon BM, Mays D, Lipsky J, Stewart JA, Fauq A, Richelson E, Pharmacokinetics and tissue distribution of a peptide nucleic acid after intravenous administration. Antisense and Nucleic Acid Drug Development 2002, 12, 65-70.
57. Kristensen E, In vitro and in vivo studies on pharmacokinetics and metabolism of PNA constructs in rodents. In Peptide Nucleic Acids: Methods and Protocols, ed. Nielsen PE, Humana Press, Totowa, NJ, 2002, pp. 259-269.
58. Ganguly S, Chaubey B, Tripathi S, Upadhyay A, Neti PV, Howell RW, Pandey VN, Pharmacokinetic analysis of polyamide nucleic-acid-cell penetrating peptide conjugates targeted against HIV-1 transactivation response element. Oligonucleotides 2008, 18, 277-286.
59. Nielsen PE, Peptide nucleic acid (PNA): a model structure for the primordial genetic material. Origins of Life and Evolution of the Biosphere 1993, 23, 323-327.
60. Böhler C, Nielsen PE, Orgel LE, Template switching between PNA and RNA oligonucleotides. Nature 1995, 376, 578-581.
61. Schmidt JG, Nielsen PE, Orgel LE, Information transfer from peptide nucleic acids to RNA by template-directed syntheses. Nucleic Acids Research 1997, 25, 4797-4802.
62. Nelson KE, Levy M, Miller SL, Peptide nucleic acids rather than RNA may have been the first genetic molecule. Proceedings of the National Academy of Sciences of the United States of America 2000, 97, 3868-3871.
63. Meierhenrich UJ, Caro GMM, Bredehö ft JH, Jessberger EK, Thiemann WHP, Identification of diamino acids in the Murchison meteorite. Proceedings of the National Academy of Sciences of the United States of America 2004, 101, 9182-9186.
64. Rasmussen S, Bedau MA, Chen L, Deamer D, Krakauer DC, Packard NH et al. (eds), Protocells, Bridging Nonliving and Living Matter, MIT Press, Cambridge, MA, 2008.
65. Braganra SM, Azevedo NF, Simoes LC, Keevil CW, Vieira MJ, Use of fluorescent in situ hybridization for the visualization of Helicobacter pylori in real drinking water biofilms. Water Science and Technology 2007, 55, 387-393.
66. Reller ME, Mallonee AB, Kwiatkowski NP, Merz WG, Use of peptide nucleic acid-fluorescence in situ hybridization for definitive, rapid identification of five common Candida species. Journal of Clinical Microbiology 2007, 45, 3802-3803.
67. Forrest GN, Roghmann MC, Toombs LS, Johnson JK, Weekes E, Lincalis DP, Venezia RA, PNA FISH for hospital acquired enterococcal bacteremia: delivering earlier effective antimicrobial therapy. Antimicrobial Agents and Chemotherapy 2008, 52, 3558-3563.
68. Ørum H, Nielsen PE, Egholm M, Berg RH, Buchardt O, Stanley C, Single base pair mutation analysis by PNA directed PCR clamping. Nucleic Acids Research 1993, 21, 5332-5336.
69. Galbiati S, Foglieni B, Travi M, Curcio C, Restagno G, Sbaiz L, Smid M, Pasi F, Ferrari A, Ferrari M, Cremonesi L, Peptide-nucleic acid-mediated enriched polymerase chain reaction as a key point for non-invasive prenatal diagnosis of beta-thalassemia. Haematologica 2008, 93, 610-614.
70. Miyake M, Sugano K, Kawashima K, Ichikawa H, Hirabayashi K, Kodama T, Fujimoto H, Kakizoe T, Kanai Y, Fujimoto K, Hirao Y, Sensitive detection of FGFR3 mutations in bladder cancer and urine sediments by peptide nucleic acid-mediated real-time PCR clamping. Biochemical and Biophysical Research Communications 2007, 362, 865-871.
71. Miyazawa H, Tanaka T, Nagai Y, Matsuoka M, Sutani A, Udagawa K, Zhang J, Hirama T, Murayama Y, Koyama N, Ikebuchi K, Nagata M, Kanazawa M, Nukiwa T, Takenoshita S, Kobayashi K, Hagiwara K, Peptide nucleic acidlocked nucleic acid polymerase chain reaction clamp-based detection test for gefitinib-refractory T790M epidermal growth factor receptor mutation. Cancer Science 2008, 99, 595-600.
72. Liu ZC, Shin DS, Shokouhimehr M, Lee KN, Yoo BW, Kim YK, Lee YS, Light-directed synthesis of peptide nucleic acids (PNAs) chips. Biosensors and Bioelectronics 2007, 22, 2891-2897.
73. Pouchain D, Diaz-Mochon JJ, Bialy L, Bradley M, A 10,000 member PNA-encoded peptide library for profiling tyrosine kinases. ACS Chemical Biology 2007, 2, 810-818.
74. Winssinger N, Damoiseaux R, Tully DC, Geierstanger BH, Burdick K, Harris JL, PNA-encoded protease substrate microarrays. Chemistry and Biology 2004, 11, 1351-1360.
75. Urbina HD, Debaene F, Jost B, Bole-Feysot C, Mason DE, Kuzmic P, Harris JL, Winssinger N, Self-assembled small-molecule microarrays for protease screening and profiling. ChemBioChem 2006, 7, 1790-1797.
76. Debaene F, Da Silva JA, Pianowski Z, Duran FJ, Winssinger N, Expanding the scope of PNA-encoded libraries: divergent synthesis of libraries targeting cysteine, serine and metallo-proteases as well as tyrosine phosphatases. Tetrahedron 2007, 63, 6577-6586.